Official Journal December 2021

Citation: A97
Online publication date: 23.12.2021

EUROPEAN PATENT OFFICE


Information from the EPO

Notice from the European Patent Office dated 9 December 2021 concerning the filing of sequence listings

1. This notice complements the decision of the President dated 9 December 2021 on the filing of sequence listings ("decision of the President"), which enters into force on 1 July 2022. It describes the procedure under the EPC and PCT for the filing of sequence listings and reflects the changes in practice brought about by the transition to WIPO Standard ST.26.

I. European patent grant procedure

Filing of sequence listings

2. If nucleotide or amino acid sequences are contained in the application documents and thus disclosed in a European patent application, the description must contain a sequence listing complying with WIPO Standard ST.26 (Rule 30(1) EPC in conjunction with Article 1 of the decision of the President).

3. WIPO Standard ST.26 is the internationally agreed standard for the presentation of nucleotide and amino acid sequence listings using XML (eXtensible Markup Language). The current version of the standard is available on the WIPO website.[ 1 ] It describes the formal requirements for the filing of sequence listings and explains how the sequences contained in a sequence listing are to be presented.

4. Following any revision of WIPO Standard ST.26, the President will decide on a date from which the revised version will apply. This information will be published in the Official Journal together with any transitional provisions concerning the furnishing of sequence listings on or after that date in relation to applications filed prior to that date (Article 1(5) of the decision of the President).

5. The EPO recommends that applicants use the WIPO Sequence software to generate WIPO Standard ST.26-compliant sequence listings. The software can be downloaded free of charge from the WIPO website. Using the latest version of this desktop application makes it easier to prepare sequence listings that comply with the requirements of the standard. Applicants are free to use other software to prepare sequence listings. In such cases, they should use the sequence listing validation function of the WIPO Sequence software to verify whether the sequence listing complies with the standard. They should also use this function to check the correctness and completeness of the sequence listing, even if it has been prepared using the WIPO Sequence software.

6. For applications with a filing date on or after 1 July 2022, sequence listings must be submitted as a single XML file using the document type definition (DTD) presented in Annex II of WIPO Standard ST.26. Sequence listings may not be filed on paper or in PDF or TXT format (Article 1 of the decision of the President). If two or more sequence listings are filed on the filing date, only the standard-compliant sequence listing will be used as the basis for the search.

7. A standard-compliant sequence listing must be filed for all sequence information that conforms to the length thresholds defined in WIPO Standard ST.26, paragraphs 7-8, irrespective of whether this sequence information is claimed or not. If the European patent application discloses nucleotide or amino acid sequences that are fragments or variants of a prior-art sequence, a standard-compliant sequence listing must be filed for these sequence fragments or variants. By way of exception, sequences which belong to the prior art and can be found in publicly accessible sequence databases do not need to be included in the sequence listing if they have been identified by their database accession number and either the version number or the database release number in the application as originally filed. This exception applies even if reference is made to these sequences in one or more claims or if the sequences are essential features of the invention or necessary for the prior-art search.[ 2 ]

8. If reference is made to a previously filed application containing a sequence listing as part of the description under Rule 40(1)(c) EPC (Box 26 of Form 1001) applicants should note that if the sequence listing contained in the previously filed application does not comply with the standard, they will be invited to furnish one that is standard-compliant (see Guidelines for Examination in the EPO ("Guidelines"), A-IV, 5.2 for further details).

9. A sequence listing filed on the filing date is part of the description. When calculating the additional fee under Rule 38(2) EPC and Article 2, item 1a RFees, the pages of the sequence listing are disregarded if the listing is filed as a separate part of the description in XML format as required by WIPO Standard ST.26. If the sequence information in the sequence listing is reproduced in the description or in other parts of the application as filed, or is submitted as an image or in PDF format, contrary to the recommendation in the standard, then the pages concerned will be taken into account in the calculation of the additional fee (Guidelines A-III, 13.2).

10. Without prejudice to Rule 30 EPC, a sequence listing forming part of the description may be corrected or amended in accordance with Rule 139 and/or Article 123(2) EPC. In such cases, a complete new WIPO Standard ST.26-compliant sequence listing containing the corrections or amendments is to be filed.

Subsequently filed sequence listings – late furnishing fee – loss of rights

11. If the applicant does not file a WIPO Standard ST.26-compliant sequence listing on the date of filing of the European patent application, or if the filed sequence listing is not standard-compliant, a standard-compliant listing must be submitted. The Receiving Section will invite the applicant to file a standard-compliant sequence listing and to pay the late furnishing fee within a non-extendable period of two months (Rule 30(3) EPC). The communication will also indicate any identified deficiencies.

12. Where the applicant fails to file a WIPO Standard ST.26-compliant sequence listing and to pay the late furnishing fee in due time, the application will be refused (Rule 30(3) EPC). This also applies if a sequence listing is subsequently filed in XML format but still contains other deficiencies with respect to the standard that were not remedied in the reply to the invitation under Rule 30(3) EPC. As a rule, only one invitation under Rule 30(3) EPC is issued. A further invitation under Rule 30(3) EPC will only be issued if the first invitation did not draw attention to all the deficiencies.[ 3 ] No late furnishing fee is due if a standard-compliant sequence listing is filed after the date of filing but before the Receiving Section has issued the communication under Rule 30(3) EPC.

13. If an application is refused under Rule 30(3) EPC, the applicant can request further processing under Article 121 and Rule 135 EPC. A further processing fee is payable for each omitted act. The filing of a WIPO Standard ST.26-compliant sequence listing and the payment of the late furnishing fee are considered to be separate acts (Guidelines E-VIII, 2).

14. A subsequently filed sequence listing may contain only the sequence information – in standardised form – contained in the original application documents. It may contain neither more nor fewer sequences than the number of sequences disclosed in the original description, and the numbering of the sequences must remain unchanged. The applicant must submit a statement to that effect (Article 2(2) of the decision of the President). It is recommended that the statement be worded as set out in the footnote.[ 4 ]

15. A sequence listing filed after the date of filing is not part of the description and therefore cannot be used to determine the originally disclosed content of the application (Rule 30(2) EPC). It can only be used for the purposes of the search, and will not be published with either the application documents or the patent specification.

Divisional applications

16. The procedure set out in points 2-15 applies, mutatis mutandis, to European divisional applications unless otherwise provided hereafter. As an independent European patent application, a divisional application must also satisfy the requirements of Rule 30 EPC in conjunction with the decision of the President.[ 5 ] Consequently, a sequence listing forming part of the description of a divisional application filed on or after 1 July 2022 must comply with WIPO Standard ST.26.

17. If a sequence listing is to form part of the description of the divisional application, it must be submitted on the date of filing with the other documents making up the divisional application. The only exception is when reference is made to a previously filed application containing a sequence listing as part of the application under Rule 40(1)(c) EPC (see point 8).

18. Where the applicant of a divisional application has filed a WIPO Standard ST.26-compliant sequence listing in the earlier application (parent application), the EPO will, upon request, add it to the file of the divisional application. This sequence listing will be used for search purposes only. It will not form part of the description of the divisional application. To facilitate the procedure, the corresponding checkbox in the EPO online filing tools and in EPO Form 1001 is pre-crossed so that a separate request does not need to be filed. Furthermore, the following is noted:

− The EPO will not follow the above procedure if the applicant, of its own motion, files a WIPO Standard ST.26-compliant sequence listing as part of the application documents of the divisional application.

− Sequence listings in the earlier (parent) application complying with earlier standards (e.g. WIPO Standard ST.25) will not be added to the file of the divisional application. In such cases, applicants must file a WIPO Standard ST.26-compliant sequence listing in the divisional application.

II. Procedure before the EPO as international authority under the PCT

19. International applications filed on or after 1 July 2022 disclosing nucleotide and/or amino acid sequences must include a sequence listing part of the description complying with WIPO Standard ST.26 (Rule 5.2 PCT). If a standard-compliant sequence listing is not available to the EPO as International Searching Authority (ISA), Supplementary International Searching Authority (SISA) or International Preliminary Examining Authority (IPEA), it will invite the applicant to furnish to it such a sequence listing under Rule 13ter.1(a) PCT within a non-extendable period of one month from the date of the invitation (Article 4 of the decision of the President).

20. The furnishing of a sequence listing in response to an invitation by the EPO as ISA, SISA or IPEA under Rule 13ter.1(a) or 13ter.2 PCT is subject to the payment of the late furnishing fee fixed by the President (Rule 13ter.1(c) PCT and Article 4 of the decision of the President). The late furnishing fee may be refunded only where the amount was paid by mistake or without cause, or the amount paid was in excess of the amount due (Agreement between the EPO and the IB of WIPO, Annex D, Part II, paragraph (1)[ 6 ]).

21. Any WIPO Standard ST.26-compliant sequence listing furnished by the applicant under Rule 13ter PCT for the purposes of the search only must be accompanied by a statement to the effect that the sequence listing does not include matter which goes beyond the disclosure in the international application as filed (Administrative Instructions under the PCT, Annex C, paragraph 39). Any sequence listing furnished under Rule 13ter PCT is not part of the international application.

22. If the applicant fails to furnish the required WIPO Standard ST.26-compliant sequence and pay the late furnishing fee due within the period under Article 4 of the decision of the President, the EPO as ISA will not issue any further invitation to furnish the sequence listing, and will search the international application only to the extent that a meaningful search can be carried out without the sequence listing (Rule 13ter.1(d) PCT). In such cases, the international search report will either indicate that certain claims were found unsearchable or will be replaced by the declaration under Article 17(2)(a) PCT. However, if the standard-compliant sequence listing is received and the late furnishing fee paid after the applicable period yet before the start of the international search, the standard-compliant sequence listing will be considered as having been received within that period.

23 If, contrary to the statement referred to in point 21 above, the EPO as ISA finds that the sequence listing in XML format furnished under Rule 13ter PCT goes beyond the disclosure in the application as originally filed, it will indicate that finding in the international search report and will proceed under point 22 above, as if the sequence listing in XML format had not been furnished under Rule 13ter PCT.

24. If a sequence listing is found to be deficient within the meaning of Article 3(1) or (2) of the decision of the President, the applicant will be invited to submit a replacement listing within the period under Article 4 of the decision of the President or, if such an invitation has already been issued, within the time remaining in the period stipulated in the invitation (point 22 above).

25. If the international search report has not been drawn up either in full or in part (point 22 above), the EPO as IPEA will perform an international preliminary examination only to the extent that a meaningful examination can be carried out (Rule 66.1(e) PCT). The applicant will be informed accordingly and an entry made in the international preliminary examination report (Rules 66.2(a)(vii) and 70.12(iv) PCT). In such cases, the EPO as IPEA will not invite the applicant to furnish a sequence listing.

26. If, after receipt of the documents specified in Rule 45bis.4(e)(i) to (iv) PCT, the EPO as SISA finds that a WIPO Standard ST.26-compliant sequence listing is not available to it, it will proceed as above, in particular as set out under point 19. The EPO as SISA will start the supplementary international search in accordance with Rule 45bis.5(a) PCT only if a standard compliant sequence listing is available to it, i.e. if it is furnished to the International Bureau of WIPO under Rule 45bis.1(c)(ii) PCT and thereafter transmitted to the EPO under Rule 45bis.4(e)(iii) (Agreement between the EPO and the IB of WIPO, Annex B, paragraph (3)[ 7 ]).

III. Procedure before the EPO as designated or elected Office (European phase)

27. WIPO Standard ST.26 applies to all Euro-PCT applications with an international filing date of 1 July 2022 or later. For international applications with an earlier international filing date, WIPO Standard ST.25 continues to apply, even if the European phase is entered after 1 July 2022 (see Article 6 of the decision of the President dated 9 December 2021 and section V below).

28. If a WIPO Standard ST.26-compliant sequence listing is contained in the international application under Rule 5.2 PCT, furnished to the EPO under Rule 13ter.1(a) PCT or otherwise available to the EPO, the applicant does not have to submit it again upon entry into the European phase.

29. Where the international application was not published in an official language of the EPO, the applicant must furnish a translation of the published application within a period of 31 months from the date of filing or, if priority has been claimed, from the earliest priority date. One of the aims of the new standard is, however, to limit the situations in which a translation of the sequence listing is required.

30. The majority of the content in a standard-compliant sequence listing must be provided using the ʺcontrolled vocabularyʺ listed in Annex 1 of WIPO Standard ST.26. Controlled vocabulary is considered to be language-independent, i.e. contained in any or all of the EPO's official languages, and thus does not need to be translated upon entry into the European phase.

31. The remaining qualifiers in a standard-compliant sequence listing are considered to be ʺlanguage-dependentʺ because they are not restricted to controlled vocabulary (WIPO Standard ST.26, points 85-88 and Annex I, Sections 6 and 8). Applicants must provide these qualifiers in one of the EPO's official languages. The standard allows these ʺlanguage-dependantʺ qualifiers to be provided in two languages within the same sequence listing. If two versions are provided, one must be in English. A translation does not have to be filed if either of the two versions of the ʺlanguage-dependantʺ qualifiers is English or the EPO official language in which the international application was published. Where multiple versions of the language-dependent qualifiers are present, the standard also allows applicants to indicate which language is to be considered the original language.

32. If the ʺlanguage-dependentʺ qualifiers are not available in English or the EPO official language in which the international application was published, then a translation of the sequence listing must be submitted upon entry into the European phase. This is to be done by filing a WIPO Standard ST.26-compliant sequence listing with the ʺlanguage-dependentʺ qualifiers in English or the EPO official language into which the other application documents have been translated.

33. If a WIPO Standard ST.26-compliant sequence listing is not available to the EPO on the expiry of the period under Rule 159(1) EPC, the applicant will be invited to file one and to pay the late furnishing fee within a period of two months from notification of the invitation (Rule 163(3) EPC in conjunction with Article 5 of the decision of the President). This period cannot be extended. Rule 30(2) and (3) EPC and Article 2 of the decision of the President apply mutatis mutandis.

34. If the deficiencies are not remedied and/or the late furnishing fee is not paid in due time, the application will be refused (Rule 30(3) EPC). The applicant may request further processing of the application under Article 121 EPC (see point 13 of this notice).

IV. Publication and notification of sequence listings

35. Where a sequence listing is to be published with the application documents (Rule 68(1) EPC; Article 153(4) EPC) or as part of the patent specification (Rule 73 EPC) (Article 1(2) of the decision of the President), it will be published in the format in which it was received.

36. A sequence listing filed after the date of filing, i.e. for search purposes only, will not be published with either the application documents or the patent specification because it is not part of the description (Rule 30(2) EPC).

37. Where the application documents on which the examining division intends to grant a patent include an XML format sequence listing, that sequence listing in XML format is contained in the communication under Rule 71(3) EPC. For applicants who have activated their Mailbox, the XML sequence listing will appear in the Mailbox along with the other documents on which the examining division intends to grant a patent. For applicants who have not activated the Mailbox, a hyperlink via which the sequence listing in XML format can be downloaded will be included in the communication sent by post.

V. Applications filed before 1 July 2022

38. WIPO Standard ST.26 does not apply to European and international applications filed before 1 July 2022. Instead, these applications must continue to comply with WIPO Standard ST.25 upon entry into the European phase and in the event of corrections, rectifications, amendments or translations being made. The provisions of the decision of the President dated 28 April 2011 on the filing of sequence listings continue to apply for these applications (see Article 6(2) of the decision of the President dated 9 December 2021 on the filing of sequence listings).

39. Upon entry into the European phase, the pages of any WIPO Standard ST.25-compliant sequence listing filed in TXT format as a separate part of the description will be excluded when calculating the additional fee under Rule 38(2) EPC and Article 2, item 1a RFees.

40. Any corrections, rectifications, amendments or translations of a WIPO Standard ST.25-compliant sequence listing are to be made by filing a complete new Standard ST.25-compliant sequence listing in TXT format containing the relevant changes (Article 123(2) EPC, Rule 39 EPC, Article 34 PCT and Rule 91 PCT).

41. Where the examining division intends to grant a patent which contains a sequence listing part of the description in TXT format, that sequence listing in TXT format will be included in the communication under Rule 71(3) EPC. Paragraph 37 applies mutatis mutandis.

VI. Entry into force and effect of previous notices from the EPO

42. The present notice supersedes the notice from the European Patent Office dated 18 October 2013 concerning the filing of sequence listings (OJ EPO 2013, 542) with effect from its entry into force on 1 July 2022.

 

 

[ 1 ] wipo.int/standards/en/part_03_standards.html.

[ 2 ] J 8/11 of 30 January 2013.

[ 3 ] J 7/11 of 24 January 2012, point 10 of the Reasons.

[ 4 ] "I hereby declare that the sequence listing does not go beyond the content of the application as filed."

[ 5 ] G 1/05, point 3.1 of the Reasons.

[ 6 ] OJ EPO 2017, A115 and 2020, A35.

[ 7 ] OJ EPO 2017, A115.

Quick Navigation